1887

Abstract

In the present study, we attempt to clarify the taxonomic positions of and . The 16S rRNA gene sequence similarity between DSM 9789 and DSM9790 (99.4 %) was above the threshold value (98.6 %) for bacterial species delineation. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between DSM 9789 and DSM9790 were higher than the threshold values (95–96 % for ANI and 70 % for dDDH) for bacterial species delineation. The present results indicate that Zillig . 1996 is a later heterotypic synonym of Schleper . 1996.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31972856, 91951205 and 32061143043)
    • Principle Award Recipient: Wen-JunLi
  • Post-doctorate fellowship under Kasetsart University Reinventing University Program (Award 2022)
    • Principle Award Recipient: ManikPrabhu Narsing Rao
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005851
2023-04-19
2024-05-12
Loading full text...

Full text loading...

References

  1. Reysenbach AL. Order I. Thermoplasmatales ord. nov. In Boone DR, Castenholz RW, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 1 New York: Springer; 2001 pp 335–340
    [Google Scholar]
  2. Darland G, Brock TD, Samsonoff W, Conti SF. A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 1970; 170:1416–1418 [View Article] [PubMed]
    [Google Scholar]
  3. Schleper C, Puhler G, Klenk H-P, Zillig W. Picrophilus oshimae and Picrophilus torridus fam. nov., gen. nov., sp. nov., two species of hyperacidophilic, thermophilic, heterotrophic, aerobic archaea. Int J Syst Bacteriol 1996; 46:814–816 [View Article]
    [Google Scholar]
  4. Golyshina OV, Pivovarova TA, Karavaiko GI, Kondratéva TF, Moore ER et al. Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the archaea. Int J Syst Evol Microbiol 2000; 50 Pt 3:997–1006 [View Article] [PubMed]
    [Google Scholar]
  5. Golyshina OV, Yakimov MM, Lünsdorf H, Ferrer M, Nimtz M et al. Acidiplasma aeolicum gen. nov., sp. nov., a euryarchaeon of the family Ferroplasmaceae isolated from a hydrothermal pool, and transfer of Ferroplasma cupricumulans to Acidiplasma cupricumulans comb. nov. Int J Syst Evol Microbiol 2009; 59:2815–2823 [View Article] [PubMed]
    [Google Scholar]
  6. Golyshina OV, Lünsdorf H, Kublanov IV, Goldenstein NI, Hinrichs K-U et al. The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales. Int J Syst Evol Microbiol 2016; 66:332–340 [View Article] [PubMed]
    [Google Scholar]
  7. Schleper C, Puehler G, Holz I, Gambacorta A, Janekovic D et al. Picrophilus gen. nov., fam. nov.: a novel aerobic, heterotrophic, thermoacidophilic genus and family comprising archaea capable of growth around pH 0. J Bacteriol 1995; 177:7050–7059 [View Article] [PubMed]
    [Google Scholar]
  8. Hawkes RB, Franzmann PD, O’Hara G, Plumb JJ. Ferroplasma cupricumulans sp. nov., a novel moderately thermophilic, acidophilic archaeon isolated from an industrial-scale chalcocite bioleach heap. Extremophiles 2006; 10:525–530 [View Article] [PubMed]
    [Google Scholar]
  9. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  10. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  11. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
    [Google Scholar]
  12. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  16. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
    [Google Scholar]
  17. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  19. Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG et al. Anvi’o: an advanced analysis and visualization platform for omics data. PeerJ 2015; 3:e1319 [View Article] [PubMed]
    [Google Scholar]
  20. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  21. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
    [Google Scholar]
  22. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12 [View Article] [PubMed]
    [Google Scholar]
  23. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  24. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  25. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  26. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  28. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005851
Loading
/content/journal/ijsem/10.1099/ijsem.0.005851
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error